IIRC the "water-like" cloak sound only appears for the two submarines in Aftermath all other vehicles and infantry (wich is also cloakable in AM) use the sound of the iron curtain. They couldnt replace it for one mission where you use Subs and the Phase Transport at the same time
As for your nuke. I would keep it for the nuke Silo. Make the SpyPlane Invisible to everyone Give it an weapon with incredibile Range and a warhead that looks like the complete Ion Cannon animation. You can still use Paratroopers (by setting the Passengers of the badger to "0" or the Parabombs as an Airstrike.
PS. @Nyerguds I saw some fantastic screens of ra2cc while lurking ur site. did u do that just by changing the palette? if yes could u email it to me pleeeeease :-)
mail is glouf [at] gmx (dot) de